This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The aim of our continuing studies is to push the boundaries of atomistic biomolecular simulation methods with a goal to expose deficiencies in the force fields and methods. We apply well-known and optimized simulation methods including AMBER and NAMD. The biomolecular simulation methods, when applied in a proper and consistent manner (utilizing the appropriate parameters and methods), allow us to better understand the structure, dynamics, interactions and energetics of proteins and nucleic acids.